How to highlight parts of my scene - strategy for materials?
I'm answering my own question as none of the answers was quite what I was looking for, but there were gems in there that let me figure it out. Thanks to all those who answered!

My solution:


I forked local copies of materials, e.g. Aluminum is now Aluminum.Gearbox, Aluminum.Manifold, etc. Thankfully, no component has more than 4 materials, so this was much less painful than I was thinking it might be.
I created my orange highlight material (some glossy, some diffuse and some emissive), using a node group to make it easy to place in all the materials where I want it.
I added a mix shader node before the output of these forked materials, and hung the orange color on the other input.
I added an empty, such as "EMPTY_gearbox_highlighter" with a custom property of "Highlight_Strength", going from 0.000 to 1.000.
I added simple drivers on the Fac of the mix shaders for all the materials in the gearbox, to be directly controlled by the Highlight_Strength property on the empty.


I'll repeat this for each highlightable component, and then all I need to do is to animate the Highlight_Strength properties on my empties, and it'll fade all the materials in the gearbox (or other component) to orange, which is exactly what I want!

Thanks to all who gave me the stepping stones to get here!

Here's the gearbox unhighlighted:



And here it is highlighted, just by taking that single custom parameter to 1.000: